\section{/home/msneddon/eclipse/galileoSR1\_\-cpp/workspace/NFsim/src/NFinput/NFinput.cpp File Reference}
\label{NFinput_8cpp}\index{/home/msneddon/eclipse/galileoSR1\_\-cpp/workspace/NFsim/src/NFinput/NFinput.cpp@{/home/msneddon/eclipse/galileoSR1\_\-cpp/workspace/NFsim/src/NFinput/NFinput.cpp}}


{\tt \#include \char`\"{}NFinput.hh\char`\"{}}\par
{\tt \#include $<$algorithm$>$}\par
\subsection*{Functions}
\begin{CompactItemize}
\item 
{\bf System} $\ast$ {\bf NFinput::initializeFromXML} (string filename, bool blockSameComplexBinding, int globalMoleculeLimit, bool verbose, int \&suggestedTraversalLimit)
\begin{CompactList}\small\item\em Maintains information about a \doxyref{component}{p.}{classNFinput_1_1component} of a TemplateMolecule. \item\end{CompactList}\item 
bool {\bf NFinput::initParameters} ({\bf TiXmlElement} $\ast$pListOfParameters, {\bf System} $\ast$s, map$<$ string, double $>$ \&parameter, bool verbose)
\begin{CompactList}\small\item\em Reads the parameter XML block and puts them in the parameter map. \item\end{CompactList}\item 
bool {\bf NFinput::initMoleculeTypes} ({\bf TiXmlElement} $\ast$pListOfMoleculeTypes, {\bf System} $\ast$system, map$<$ string, int $>$ \&allowedStates, bool verbose)
\begin{CompactList}\small\item\em Reads the MoleculeType XML block and adds the MoleculeTypes to the system. \item\end{CompactList}\item 
bool {\bf NFinput::initStartSpecies} ({\bf TiXmlElement} $\ast$pListOfSpecies, {\bf System} $\ast$system, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, bool verbose)
\begin{CompactList}\small\item\em Reads a Species XML block, creates the molecules and adds them to the system. \item\end{CompactList}\item 
bool {\bf NFinput::initReactionRules} ({\bf TiXmlElement} $\ast$pListOfReactionRules, {\bf System} $\ast$system, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, bool blockSameComplexBinding, bool verbose, int \&suggestedTraversalLimit)
\begin{CompactList}\small\item\em Reads a reactionRule XML block and adds the rules to the system. \item\end{CompactList}\item 
bool {\bf NFinput::readObservableForTemplateMolecules} ({\bf TiXmlElement} $\ast$pObs, string observableName, vector$<$ {\bf TemplateMolecule} $\ast$ $>$ \&tmList, vector$<$ string $>$ \&stochRelation, vector$<$ int $>$ \&stochQuantity, {\bf System} $\ast$s, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, int obsType, bool verbose, int \&suggestedTraversalLimit)
\item 
bool {\bf NFinput::initObservables} ({\bf TiXmlElement} $\ast$pListOfObservables, {\bf System} $\ast$system, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, bool verbose, int \&suggestedTraversalLimit)
\begin{CompactList}\small\item\em Reads an observable XML block and adds the new observables to the system. \item\end{CompactList}\item 
{\bf TemplateMolecule} $\ast$ {\bf NFinput::readPattern} ({\bf TiXmlElement} $\ast$pListOfMol, {\bf System} $\ast$s, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, string patternName, map$<$ string, {\bf TemplateMolecule} $\ast$ $>$ \&templates, map$<$ string, {\bf component} $>$ \&comps, map$<$ string, {\bf component} $>$ \&symMap, bool verbose, int \&suggestedTraversalLimit)
\begin{CompactList}\small\item\em Reads a pattern XML block and returns the set of new TemplateMolecule objects. \item\end{CompactList}\item 
bool {\bf NFinput::readProductPattern} ({\bf TiXmlElement} $\ast$pListOfMol, {\bf System} $\ast$s, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, string patternName, vector$<$ {\bf MoleculeType} $\ast$ $>$ \&productMoleculeTypes, vector$<$ vector$<$ int $>$ $>$ \&stateInformation, vector$<$ vector$<$ int $>$ $>$ \&bindingSiteInformation, bool verbose)
\begin{CompactList}\small\item\em Reads a pattern XML block and returns the set of new TemplateMolecule objects. \item\end{CompactList}\item 
bool {\bf NFinput::readProductMolecule} ({\bf TiXmlElement} $\ast$pMol, {\bf System} $\ast$s, map$<$ string, double $>$ \&parameter, map$<$ string, int $>$ \&allowedStates, string patternName, vector$<$ {\bf MoleculeCreator} $\ast$ $>$ \&moleculeCreatorsList, map$<$ string, {\bf component} $>$ \&comps, bool verbose)
\begin{CompactList}\small\item\em Reads a product molecule XML block and returns a TemplateMolecule objects. \item\end{CompactList}\end{CompactItemize}
